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cDNA sequence analysis and characterization of a cytokine-inducing monoclonal antibody derived from autoimmune MRL/MP-lpr/lpr mouse.

We have previously reported that a monoclonal antibody 1D11 derived from an autoimmune MRL/Mp-lpr/lpr (MRL/lpr) mouse induced synthesis or increased production of IL-3, IL-6, and TNF-alpha in the IL-3-dependent bone marrow-derived cell line FDC-P2/185-4. In this report, we analyzed a sequence of cDNA encoding the V region of 1D11, and found that VH and VL segments of 1D11 belonged to the J558 and V kappa 21 family, respectively. The nucleotide sequence of 1D11 in the VH segment was highly homologous to that of AM9, a monoclonal RF derived from MRL/lpr mouse, and the only difference was the replacement of 3 nucleotides in the framework region 1 (FR1). However, the deduced amino acid sequence of 1D11 was identical to that of AM9. In contrast with the VH segment, the sequences of the VL regions of these two antibodies were quite different from each other; 1D11 showed a 3 base deletion in the FR2 and a 24 base insertion in the FR3 compared with AM9. At present, the mechanisms of such insertions or deletions in the FRs of autoantibodies are almost unknown. It is generally accepted that the differences in specificity and affinity of these autoantibodies depend on differences of CDR sequence. However, it is possible that not only CDRs but also FRs of autoantibodies play a critical role in pathogenicity and/or specificity in autoimmune diseases.

Amino Acid Sequence↗

Cloning and expression analysis of full length mouse cDNA sequences encoding the transformation associated protein p53.

We have cloned and sequenced overlapping cDNA fragments which together encode the entire mouse protein p53. Using these cDNA's we have reconstructed the full length coding region for the protein, and have analysed its coding potential by expression in vitro, both as a full length sequence and as a subfragment contained in a fusion protein. The predicted amino acid sequence contains no obvious homologies to any known oncogenes but includes a possible tyrosine kinase acceptor site.

Amino Acid Sequence↗

Partial cDNA sequence encoding a globular domain at the C terminus of the rat cartilage proteoglycan.

We have isolated and sequenced a cDNA clone of 872 base pairs from the 3' end of the mRNA for the large cartilage specific proteoglycan from rat. Identification was confirmed by a comparison with published protein sequence. Hybridization analysis shows the presence of an 8-9-kilobase mRNA for this proteoglycan in rat and chick sternal chondrocytes and rat chondrosarcoma cells, but not in RNA from rat fibroblasts, vitamin A-treated chick chondrocytes, chick crop, or bone. The carboxyl portion of the proteoglycan is deduced to terminate in a globular domain, which includes a region homologous to a chick hepatic lectin, and is possibly involved in binding to N-acetylglucosamine. The clone extends into a region where serines are clustered, probably the start of the chondroitin sulfate-rich region.

Amino Acid Sequence↗

Identification and cDNA sequence of delta-preprotachykinin, a fourth splicing variant of the rat substance P precursor.

The neuropeptides substance P and neurokinin A are synthesised from a family of precursor polypeptides encoded by the preprotachykinin A (PPT) gene. In addition to a mRNA (beta-PPT) containing all 7 exons of the gene, alternatively spliced mRNAs lacking either exon 4 (gamma-PPT) or exon 6 (alpha-PPT) have been identified. We have determined the sequences of cDNA clones encoding four variants of PPT mRNA from rat dorsal root ganglion (DRG), including a novel mRNA species (delta-PPT) in which both exons 4 and 6 are absent. The sequence of delta-PPT predicts the existence of a novel tachykinin precursor polypeptide.

Amino Acid Sequence↗

cDNA sequence and gene expression of storage protein-2--a juvenile hormone-suppressible hexamerin from the fall webworm, Hyphantria cunea Drury.

We isolated and sequenced a cDNA clone corresponding to storage protein-2 (SP-2) from the fall webworm, Hyphantria cunea. The cDNA for SP-2 (2572 bp) codes for a 747-residue protein with a predicted molecular mass of 88.5 kDa. The calculated isoelectric point is 7.6. Multiple alignment analysis of amino acid sequence revealed that SP-2 is most similar to BJHSP2 (74.3% identity). According to both the phylogenetic analyses and criteria for amino acid composition, SP-2 belongs to the subfamily of moderately methionine-rich storage proteins (3.2% methionine, 11.8% aromatic amino acid). Topical application of the JH analog, methoprene, after head ligation of larvae, suppressed transcription of the SP-2 gene, indicating hormonal effects at the transcriptional level. The SP-2 transcript was detected by Northern blot analysis in Malpighian tubules, in addition to the fat body where it was most abundant. The local expression of SP-2 in Malpighian tubules suggests that it may have some function in that organ.

Amino Acid Sequence↗

Characterization of 954 bovine full-CDS cDNA sequences.

BACKGROUND: Genome assemblies rely on the existence of transcript sequence to stitch together contigs, verify assembly of whole genome shotgun reads, and annotate genes. Functional genomics studies also rely on transcript sequence to create expression microarrays or interpret digital tag data produced by methods such as Serial Analysis of Gene Expression (SAGE). Transcript sequence can be predicted based on reconstruction from overlapping expressed sequence tags (EST) that are obtained by single-pass sequencing of random cDNA clones, but these reconstructions are prone to errors caused by alternative splice forms, transcripts from gene families with related sequences, and expressed pseudogenes. These errors confound genome assembly and annotation. The most useful transcript sequences are derived by complete insert sequencing of clones containing the entire length, or at least the full protein coding sequence (CDS) portion, of the source mRNA. While the bovine genome sequencing initiative is nearing completion, there is currently a paucity of bovine full-CDS mRNA and protein sequence data to support bovine genome assembly and functional genomics studies. Consequently, the production of high-quality bovine full-CDS cDNA sequences will enhance the bovine genome assembly and functional studies of bovine genes and gene products. The goal of this investigation was to identify and characterize the full-CDS sequences of bovine transcripts from clones identified in non-full-length enriched cDNA libraries. In contrast to several recent full-length cDNA investigations, these full-CDS cDNAs were selected, sequenced, and annotated without the benefit of the target organism's genomic sequence, by using comparison of bovine EST sequence to existing human mRNA to identify likely full-CDS clones for full-length insert cDNA (FLIC) sequencing. RESULTS: The predicted bovine protein lengths, 5' UTR lengths, and Kozak consensus sequences from 954 bovine FLIC sequences (bFLICs; average length 1713 nt, representing 762 distinct loci) are all consistent with previously sequenced mammalian full-length transcripts. CONCLUSION: In most cases, the bFLICs span the entire CDS of the genes, providing the basis for creating predicted bovine protein sequences to support proteomics and comparative evolutionary research as well as functional genomics and genome annotation. The results demonstrate the utility of the comparative approach in obtaining predicted protein sequences in other species.

5' Untranslated Regions↗

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov).

Algorithms↗

cDNA sequence for mouse caltractin.

Caltractin, a contractile Ca(2+)-binding protein, has not been found in any species other than algae. We now report the first isolation and sequencing of cDNA encoding mouse caltractin from a testis cDNA library by immunoscreening. Mouse caltractin has a molecular mass of 20 kDa, which is the same as that from algae.

Amino Acid Sequence↗

[Differentially expressed cDNA sequences homologous with known genes in human nasopharyngeal carcinoma].

In order to search the tumor suppressor genes correlated with pathogenesis of human nasopharyngeal carcinoma(NPC), we applied the PCR-based subtractive hybridization technique of representational difference analysis (RDA) to the primary culture cells of normal human nasopharyngeal epithelial and HNE1, a poorly differentiated NPC cell line. Following four successive subtractions of HNE1 complementary DNA from normal human nasopharyngeal epithelial cells complementary DNA, difference products were cloned into pGEM-T easy vector and nucleotide sequences determined. Comparison of cDNA sequences against the databases identified 9 known genes. Known genes included TRIP1(TGF beta receptor interacting protein), TAF, ezrin, MHC II, actinin, Histone H1 zero, Cytokeratin 13, Squalene Synthetase and RNA Synthetase-like. Some of them have an effective suppressive ability on the tumor. In this study, we have demonstrated that cDNA RDA is an effective strategy for systematically isolating differences in gene expression between two related but functionally distinct cells. Our results also indicated that the NPC includes interaction of multigenes and this experiment offers a new route for NPC research.

Carcinoma, Squamous Cell↗

Hyphantria cunea ferritin heavy chain homologue: cDNA sequence and mRNA expression.

We have sequenced a cDNA clone encoding a 26-kDa ferritin subunit, which was heavy chain homologue (HCH), in fall webworm, Hyphantria cunea. The HCH cDNA was obtained from the screening of a cDNA library using a PCR product. H. cunea ferritin is composed of 221 amino acid residues and their calculated mass is 26,160 Da. The protein contains the conserved motifs for the ferroxidase center typical for heavy chains of vertebrate ferritin. The iron-responsive element sequence with a predicted stem-loop structure is present in the 5'-untranslated region of ferritin HCH mRNA. The sequence alignment of ferritin HCH shows 68.9 and 68.7% identity with Galleria mellonella HCH (26 kDa ferritin) and Manduca sexta HCH, respectively. While G type insect ferritin vertebrate light chain homologue (LCH) is distantly related to H. cunea ferritin HCH (17.2-20.8%), the Northern blot analysis revealed that H. cunea ferritin HCH was ubiquitously expressed in various tissues and all developmental stages. The ferritin expression of midgut is more responsive to iron-fed, compared to fat body in H. cunea.

Amino Acid Sequence↗

Apis mellifera ultraspiracle: cDNA sequence and rapid up-regulation by juvenile hormone.

Two hormones, 20-hydroxyecdysone (20E) and juvenile hormone (JH) are key regulators of insect development including the differentiation of the alternative caste phenotypes of social insects. In addition, JH plays a different role in adult honey bees, acting as a 'behavioural pacemaker'. The functional receptor for 20E is a heterodimer consisting of the ecdysone receptor and ultraspiracle (USP) whereas the identity of the JH receptor remains unknown. We have cloned and sequenced a cDNA encoding Apis mellifera ultraspiracle (AMUSP) and examined its responses to JH. A rapid, but transient up-regulation of the AMUSP messenger is observed in the fat bodies of both queens and workers. AMusp appears to be a single copy gene that produces two transcripts ( approximately 4 and approximately 5 kb) that are differentially expressed in the animal's body. The predicted AMUSP protein shows greater sequence similarity to its orthologues from the vertebrate-crab-tick-locust group than to the dipteran-lepidopteran group. These characteristics and the rapid up-regulation by JH suggest that some of the USP functions in the honey bee may depend on ligand binding.

Amino Acid Sequence↗

cDNA sequence of human beta-preprotachykinin, the common precursor to substance P and neurokinin A.

The nucleotide sequence of cDNA encoding the human substance P precursor, beta-preprotachykinin (beta-PPT), has been determined. The source of mRNA was a human laryngeal carcinoid tumour that contained a high concentration of immunoreactive substance P. The human beta-PPT polypeptide is 129 amino acids long and contains regions encoding substance P and neurokinin A, each flanked by basic amino acid residues. Residues 72-107 of the human beta-PPT polypeptide encode the sequence of neuropeptide K, an N-terminally extended form of neurokinin A recently isolated from porcine brain.

Animals↗

gamma Heavy chain disease in man: cDNA sequence supports partial gene deletion model.

Human gamma heavy chain disease (HCD) is characterized by the presence in serum of a short monoclonal Ig gamma chain unattached to light chains. Although most HCD proteins have internal deletions, in some the defect is NH2-terminal. The OMM gamma 3 HCD serum protein is of the latter type, having undergone an extensive NH2-terminal deletion with a sequence starting within the hinge. A cell line synthesizing the OMM protein has enabled us to study the biogenesis of the abnormal molecule. In vitro translation of isolated mRNA yields a protein containing a hydrophobic NH2-terminal leader sequence. In the intact cell, the precursor molecule is processed normally to yield a protein with an NH2-terminal sequence homologous to the beginning of the variable (V) region. The nucleotide sequence of cDNA prepared from the OMM mRNA encodes a 19-amino acid leader followed by the first 15 residues of the V region. An extensive internal deletion encompasses the remainder of the V and the entire CH1 domain. Immediately following the short V region, there is information in the cDNA for the entire normal hinge. The primary synthetic product is thus an internally deleted molecule that undergoes postsynthetic degradation to yield the NH2-terminally deleted serum protein. The structure of the OMM mRNA suggests that the protein abnormality results from a partial gene deletion rather than defective splicing.

Amino Acid Sequence↗

Identification of a breast cancer-specific gene, BCSG1, by direct differential cDNA sequencing.

A high-throughput direct-differential cDNA sequencing approach was employed to identify genes differentially expressed in normal breast as compared with breast cancer. Approximately 6000 expressed sequence tags (ESTs) from cDNA libraries of normal breast and breast carcinoma were selected randomly and subjected to EST-sequencing analysis. The relative expression levels of more than 2000 unique EST groups were quantitatively compared in normal versus cancerous breast. Of many putative differentially expressed genes, a breast cancer-specific gene, BCSGC1, which was expressed in high abundance in a breast cancer cDNA library but scarcely in a normal breast cDNA library, was identified as a putative breast cancer marker. In situ hybridization analysis demonstrated stage-specific BCSG1 expression as follows: BCSG1 was undetectable in normal or benign breast lesions, showed partial expression in ductal carcinoma in situ, but was expressed at an extremely high level in advanced infiltrating breast cancer. The predicted amino acid sequence of BCSG1 gene has a significant sequence homology to the non-amyloid beta protein fragment of the Alzheimer's disease amyloid protein. BCSG1 overexpression may indicate breast cancer malignant progression from benign breast or in situ carcinoma to the highly infiltrating carcinoma.

Amino Acid Sequence↗

cDNA sequence and chromosomal localization of the NDUFS8 human gene coding for the 23 kDa subunit of the mitochondrial complex I.

We have sequenced the cDNA for the 23 kDa subunit of the human mitochondrial respiratory complex I. The deduced protein consists of 210 amino acids (Mr = 23705 Da) with a 34 amino acid N terminus presumably acting as a presequence for mitochondrial import. The predicted mature protein (Mr = 20290 Da) is 92% identical to the bovine mitochondrial subunit and 72% to the Rhodobacter capsulatus NUOI counterpart. Two clusters of four cysteine residues are conserved among these proteins. The gene (NDUFS8) coding for the human subunit has been mapped to chromosome 11q13.

Amino Acid Sequence↗

cDNA sequence and expression of the ceratotoxin gene encoding an antibacterial sex-specific peptide from the medfly Ceratitis capitata (diptera).

Ceratotoxins are antibacterial 3-kDa molecular mass amphiphilic peptides isolated from the female reproductive accessory glands of the medfly Ceratitis capitata. They are physiologically related to bee melittin and show amino acid sequence homology with magainin peptides. In this paper, we report the complete sequence of cDNA coding for ceratotoxin A and the expression of the gene during the life cycle of the insect. Experimental data show that the ceratotoxin is a gene expressed exclusively in the imaginal stages and that it is female-specific, related to sexual maturity, and stimulated by mating. Differently from most antibacterial insect hemolymph peptides, it is not induced by microbial infection. Western blot analysis using an anti-ceratotoxin antibody indicates the female accessory glands as the only site where the production of the ceratotoxin peptide occurs.

Amino Acid Sequence↗

The acid-stable proteinase inhibitor of human mucous secretions (HUSI-I, antileukoprotease). Complete amino acid sequence as revealed by protein and cDNA sequencing and structural homology to whey proteins and Red Sea turtle proteinase inhibitor.

The complete amino acid sequence of human antileukoprotease has been determined by direct sequencing of the inhibitory active protein isolated from seminal plasma (HUSI-I) and by sequence analysis of cDNA reverse-transcribed from mRNA prepared from cervical tissue. The inhibitor (Mr 11726) consists of 107 amino acid residues including 16 cysteines presumably forming disulfide bonds. The molecule comprises two consecutive domains which are homologous to each other, to the second domain of the basic protease inhibitor from Red Sea turtle (chelonianin) and to both domains of the whey proteins of rat and mouse. Both domains contain a pattern of cysteines known as the 'four-disulfide-core' that has also been found in wheat germ agglutinin and neurophysin.

Amino Acid Sequence↗